Genomic Surveillance of Dengue Virus During the 2024 Outbreak in a Northeastern Brazilian State

ABSTRACT

Dengue remains a major public health challenge in tropical regions, where viral genetic diversity, vector ecology and human mobility contribute to recurrent outbreaks. In 2024, Brazil experienced its largest recorded dengue epidemic, with intense transmission across the Northeast region. This study characterizes the epidemiological, genomic and phylogeographic features of dengue virus (DENV) circulation during the 2024 outbreak in Alagoas, northeastern Brazil. Of 6102 suspected cases analysed by molecular diagnostics, 1607 (26.3%) were confirmed as DENV infections. Epidemiological analyses revealed widespread transmission across 79 municipalities, marked seasonality with peak incidence between March and August, and a disproportionate burden among adolescents and young adults. DENV‐1 and DENV‐2 were the predominant serotypes, accounting for 57.1% and 42.6% of confirmed cases, respectively; three DENV‐3 infections and one DENV‐1/DENV‐2 co‐infection were also identified. Whole‐genome sequencing yielded high‐quality genomic data supporting phylogenetic and phylogeographic analyses. DENV‐1 sequences belonged to genotype V, classified into lineages E.1 and D.1.1, while DENV‐2 sequences clustered within genotype II (lineage F.1.1.2) and genotype III (lineage C.1.1). Time‐scaled phylogenetic analyses revealed multiple independent introductions of both serotypes from distinct Brazilian regions, followed by sustained local transmission and lineage expansion. Infections among non‐residents, including an international case, further underscore the role of population mobility in viral dissemination. Collectively, these findings indicate that the 2024 outbreak was driven by recurrent viral introductions combined with the persistence of locally established transmission chains, highlighting the value of integrated genomic surveillance for outbreak preparedness and public health response.